Do the fans work if you plug them into the always on fan outputs?
If no fans work when plugged into those connectors, check the 1A blade fuse.
If some fans work in those connectors but others don't, then the non-working fans are faulty, or have bad crimp connections.
If the fans work in the always-on connectors but not in some of the controlled fan connectors, then the fan control MOSFETs on the Duet may be blown. What sort of fans are they?